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Nucleic_Acid_Databases, Bioinformatics, genome
- 1. 4/21/2024 8:54 PM Introduction to Bioinformatics databases: Nucleic Acid Databases Dinesh Gupta ICGEB
- 2. 4/21/2024 8:54 PM Biological databases: why? • Need for storing and communicating large datasets has grown • Make biological data available to scientists. • To make biological data available in computer-readable form.
- 3. 4/21/2024 8:54 PM Different classifications of databases • Type of data – nucleotide sequences – protein sequences – proteins sequence patterns or motifs – macromolecular 3D structure – gene expression data – metabolic pathways
- 4. 4/21/2024 8:54 PM Different classifications of databases…. • Primary or derived databases – Primary databases: experimental results directly into database – Secondary databases: results of analysis of primary databases – Aggregate of many databases • Links to other data items • Combination of data • Consolidation of data
- 5. 4/21/2024 8:54 PM Different classifications of databases…. • Technical design – Flat-files – Relational database (SQL) – Exchange/publication technologies (FTP, HTML, CORBA, XML,...)
- 6. 4/21/2024 8:54 PM Different classifications of databases…. • Availability – Publicly available, no restrictions – Available, but with copyright – Accessible, but not downloadable – Academic, but not freely available – Proprietary, commercial; possibly free for academics
- 7. 4/21/2024 8:54 PM Where do I get DB of my interest ?
- 10. 4/21/2024 8:54 PM Nucleotide sequence databases • EMBL, GenBank, and DDBJ are the three primary nucleotide sequence databases • EMBL www.ebi.ac.uk/embl/ • GenBank www.ncbi.nlm.nih.gov/Genbank/ • DDBJ www.ddbj.nig.ac.jp
- 11. 4/21/2024 8:54 PM Genbank • An annotated collection of all publicly available nucleotide and proteins • Set up in 1979 at the LANL (Los Alamos). • Maintained since 1992 NCBI (Bethesda). • http://www.ncbi.nlm.nih.gov
- 14. 4/21/2024 8:54 PM EMBL Nucleotide Sequence Database • An annotated collection of all publicly available nucleotide and protein sequences • Created in 1980 at the European Molecular Biology Laboratory in Heidelberg. • Maintained since 1994 by EBI- Cambridge. • http://www.ebi.ac.uk/embl.html
- 17. 4/21/2024 8:54 PM DDBJ–DNA Data Bank of Japan • An annotated collection of all publicly available nucleotide and protein sequences • Started, 1984 at the National Institute of Genetics (NIG) in Mishima. • Still maintained in this institute a team led by Takashi Gojobori. • http://www.ddbj.nig.ac.jp
- 20. 4/21/2024 8:54 PM Other NCBI nucleic acids DBs • EST database: A collection of expressed sequence tags, or short, single-pass sequence reads from mRNA (cDNA). • GSS database: A database of genome survey sequences, or short, single-pass genomic sequences. • HomoloGene: A gene homology tool that compares nucleotide sequences between pairs of organisms in order to identify putative orthologs. • HTG database: A collection of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. • SNPs database: A central repository for both single-base nucleotide substitutions and short deletion and insertion polymorphisms. • RefSeq: A database of non-redundant reference sequences standards, including genomic DNA contigs, mRNAs, and proteins for known genes. Multiple collaborations, both within NCBI and with external groups, supports data-gathering efforts. • STS database: A database of sequence tagged sites, or short sequences that are operationally unique in the genome. • UniSTS: A unified, non-redundant view of sequence tagged sites (STSs). • UniGene: A collection of ESTs and full-length mRNA sequences organized into clusters, each representing a unique known or putative human gene annotated with mapping and expression information and cross-references to other sources.
- 23. 4/21/2024 8:54 PM Sequence submission • Data mainly direct submissions from the authors. • Submissions through the Internet: – Web forms. – Email. • Sequences shared/exchanged between the 3 centers on a daily basis: – The sequence content of the banks is identical.
- 24. 4/21/2024 8:54 PM Derived databases • CUTG Codon usage tabulated from GenBank http://www.kazusa.or.jp/codon/ • Genetic Codes Deviations from the standard genetic code in various organisms and organelles http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c • TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml • UniGene Unified clusters of ESTs and full-length mRNA sequences http://www.ncbi.nlm.nih.gov/UniGene/ • ASAP Alternative spliced isoforms http://www.bioinformatics.ucla.edu/ASAP • Intronerator Introns and alternative splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
- 31. 4/21/2024 8:54 PM Nucleic acid structure databases • NDB Nucleic acid-containing structures http://ndbserver.rutgers.edu/ • NTDB Thermodynamic data for nucleic acids http://ntdb.chem.cuhk.edu.hk/ • RNABase RNA-containing structures from PDB and NDB http://www.rnabase.org/ • SCOR Structural classification of RNA: RNA motifs by structure, function and tertiary interactions • http://scor.lbl.gov/
- 36. 4/21/2024 8:54 PM Database searching tips • Look for links to Help or Examples • Try Boolean searches • Be careful with UK/US spelling differences – leukaemia vs leukemia – haemoglobin vs hemoglobin – colour vs color
- 37. 4/21/2024 8:54 PM Exercises • Study the statistics of the three primary nucleic acid databases: Are they matching ? • Look for a gene of your interest in the three primary nucleic acid databases: compare the information given in each one of them. • Read NAR DB paper and NAR DB index site: search for different nucleic acid databases based on different search terms. • Self study: – http://www3.oup.co.uk/nar/database/c/ – Download NAR database paper (NARDB2004) from: ftp://cbag.sc.mahidol.ac.th/pub/Course_Materials/dinesh